When the Civil War began, although born in Virginia, he refused to resign his commission and commanded the USS Keystone State. and searched for the Confederate raider CSSSumter. This was his first command. Later he joined the West Indies Squadron searching for blockade-runners.
Then he commanded the new gunboat, USS Maratanza and took part in McClellan's Peninsula Campaign. He captured the CSS Teaser 4 July 1862.
From there he joined the blockade off Wilmington, N.C. 25 September 1862 and at one point fired on Fort Caswell.
Promoted to captain, he took command of the USS DeSoto in the East Gulf Blockading Squadron. From there,he received command of the USS Canandaigua (the ship that rescued the 150-man crew of the SS Housatonic after it was sunk by the submarine Hunley on Feb. 17, 1864).
He served with the South Atlantic Blockading Squadron until the end of the war and then commanded the USS Saranac of the Pacific Squadron inits search for the Shenandoah.